JDUB is right: don't mess with safety items like brakes. If in doubt, check it out!
It seems this only occurs when braking? Correct?
If it is a warped rotor ... did you install them or did you have them done? If someone else, take it back.
If you have done the work, you could remove them and have them turned. Yes, a bummer, but any Midas shop with turn 'em for you. Hint, find out if they are open on Sunday. Call them on Sunday and see if they would turn them for you. Around here, they will turn them for not very much money since Sundays are slow days.
The scraping sound .... hmmm is it from the front or rear?
On our '91 300E we had a very weird sound that would only come about during heavy braking from the rear. I pulled the rear wheels and found that the previous owner had installed brake pads that were square/rectangular instead of curved. The rectangular part was rubbing on the center of the brake disk, the hub part. It would only do it when it got hot enough.
I installed the correct "curved" pads and the trouble disappeared.
It seems that brake pads tend to come in similar sizes. In this case the old pads fit. They just didn't function well.
'03 E320 Wagon-Sold
'95 E320 Wagon-Went to Ex
'93 190E 2.6-Wrecked
'91 300E-Went to Ex
'65 911 Coupe (#302580)